This version is no longer in development. Switch over to a Java and Xuggle baased solution is in progress at:
https://github.com/JumpingFrog/tmv_encoder
TMV Encoder for Windows, written in C#.
Requires the AForge.NET library, quite a few things are only half implemented (e.g. audio support).
Video decompressing through - http://aforgenet.com
Audio stream stripping through - http://www.codeproject.com/Articles/7388/A-Simple-C-Wrapper-for-the-AviFile-Library